French Interior Minister Bernard Cazeneuve led the impassioned plea to EU counterparts at a meeting in Luxembourg, calling for "a European PNR (Passenger Name Record) ... and a more efficient system of checks at airports.
"This is urgent," he said.
German Interior Minister Thomas de Maizière echoed Cazeneuve, saying "three thousand fighters have left Europe to wage jihad and we don't want Europe to become an exporter of terror".
"We above all do not want battle-hardened fighters to return to Europe and plan attacks," he said. "We need measures both at the national and European levels."
Cazeneuve said a new category of "foreign fighters" should be added to the list of suspect individuals for police at European borders.
The current categories include offenders, criminals and fugitives.
The Schengen zone comprises 26 European countries, 22 EU members as well as Norway, Switzerland, Liechtenstein and Iceland.
France has Europe's biggest Muslim population and is thought to have provided the largest contingent of Western jihadists to the conflict in Syria.
Prime Minister Manuel Valls told MPs last month that around 1,000 French citizens are involved in jihadist networks, with an estimated 580 having travelled to fight in Syria and Iraq.
Around 400 men and women are thought to have left Germany for the Middle East to join jihadists.